Mendeley

Sente is still my reference manager of choice, but there is one major limitation to the way Sente works. Sente has powerful tools to identify citation information embedded on major scholarly sites. Recently they even added support for AnthroSource, which would be great news if AnthroSource hadn’t become so impossible to use since the “upgrade” back in January. But to make use of these tools you need to be using the web browser embedded within Sente. So, if Firefox is your default browser and you open up a link in an e-mail or blog post to an interesting book or scholarly article, you can’t simply add it to Sente. You have to launch Sente (if it isn’t already running), find the appropriate website, and find the book or article again. Oh, and don’t forget to properly select the library you want to import the article to…

By the time I’m done adding the citation I’ve forgotten what I was researching in the first place. Or I just don’t do it because it is too much of a pain. I want to be able to save that citation right then and there – in my browser, while I’m doing whatever it was I’m doing, without missing a beat.

Up till now there were two ways I could do this. The first was to use CiteULike, a long time favorite here at SavageMinds. But then I have the problem of merging my CiteULike collection with my Sente collection. It never works quite as well as I would like. I wish there was something like what I can do with my Bank website: “download all activity since your last download.”

Another option is the wonderful Zotero plugin for Firefox. Zotero gives you full fledged citation management software built into your browser. There is even a web service where you can sync your citations and share groups etc. There are also plugins for OpenOffice to help you format your bibliography as you write. Sounds perfect, but it has never worked for me. The biggest problem is that Firefox is already a little slow and buggy, and when I’m using Zotero it is even worse. On top of that, the sync and online features never quite worked for me. But an even bigger problem is that I’d like to be able to use Safari or Chrome as my browser as well, I don’t want to be stuck in Firefox just because of Zotero.

Finally we get to the subject of this post: Mendeley. Mendeley is still in development and I can’t recommend you use it as your main bibliographic software just yet, but of all the programs I’ve looked at and tried it is the one that fits best into my actual workflow. Mendeley is both a web application and stand alone desktop software. The two stay in perfect sync. Anyone who uses Evernote (another favorite) will be familiar with this model. That means that all you need to “install” in your web browser is a single javascript bookmarklet you can click whenever you see a citation you want to save. The bookmarklet is powerful enough that on a page of Google Scholar results you can import all the items at once (similar to how Sente works). Like Zotero, Mendeley also offers an OpenOffice plugin to create bibliographies and properly formatted in-text citations. I tested it out and it works pretty well, except that you are limited in the citation formats and there is so far no way to edit them or create your own.

While Mendeley is still a work in progress, it is already a very powerful research tool, and I have a feeling that, over time, it will eclipse the competition. At least I hope it does, because it is the first software of its kind which seems to fit perfectly into my workflow. Now if we could only get the AAA to fix AnthroSource …

How to,

15 thoughts on “Mendeley”

  1. Kerim, I am sorry that Zotero has not been working for you as you would like. I cannot say enough good things about it and the people behind it. Among its many virtues for me is that it is a free and open project with an ever growing community of supporters behind it. I anticipate smarter scholarly societies will start collaborating with CNMH (as museums are on Omeka) to make discipline-specific Zotero enhancements. Journal bibliographic styles and interoperability with discipline specific digital collections are the start of this, I think.

    Thanks for sharing your technology experiences here.

    Jason

  2. Thanks for the tip on Mendeley. I have been using Bookends and Zotero (assuming you are on a Mac since you Sente), and that seems to work pretty well. The built in browser in BE is getting more and more powerful, and Zotero grabs everything else. I don’t use CiteULike, but apparently BE has some rudimentary implementation. I also have to say that the developer has been great in working through some difficult multi-lingual issues.

  3. I’ve been dying to get away from Endnote, and Sente looks nice to me, but can it be set to work with the AAA bibliographic format?

  4. Yes, Sente (as well as Bookends and Zotero) all allow editing of bibliographic formats. Only Mendeley doesn’t (yet) have that feature.

  5. Wonderful. Do you know of a resource to import a pre-edited bibliographic AAA format for Sente?
    I’m having a bit of trouble figuring out the bibliography format editor.

  7. i’m quite impressed by mendeley – esp the folder monitoring and the internal pdf viewer w/ annotations.

    however, i’m finding that i’m increasingly citing blog posts, videos, pictures, and other online articles and for that, Zotero still beats everything else. and the sync has worked perfectly (on win, mac and linux). too bad you’re having problems with it.

    choices, choices…

  8. Fergus: Very nice!

    C.R. Sorry, I don’t know. I’ve found that the best thing to do is to find a citation format close to the one you are looking for and to tweak it, rather than starting from scratch. In many cases Chicago is a good starting point.

    Arvind & Jason: Glad to hear Zotero works for you. I tried many times to get it to work, even setting up a clean Firefox profile just for Zotero. I still found Firefox performance degraded, and sync issues. But a bigger issue for me is the ability to use Chrome or Safari if I want to – Mendeley’s browser agnostic approach seems inherently better for this reason.

    I should add that Mendeley offers built-in CiteULike synchronization of some kind, although I’m still a little unclear how well this works.

  9. Hi Karim,

    thanks for the nice review. At the moment, our focus is on polishing, stabilizing and speeding up the software – we want to leave the beta status this fall. The ability to add/edit own citation styles is also on our roadmap, though I don’t have an estimate for when this will be available (most likely later this year).

    Regarding the CiteULike sync: You can set this up by initiating the sync from your Mendeley profile (in the settings). You will then be taken to CiteULike to confirm. At the moment, the sync only works one-way (CiteULike > Mendeley), but both our teams are working on making it two-way.

    The next major Mendeley release, due in 3-4 weeks, will also include a Zotero > Mendeley sync.

    All the best,
    Victor

  10. Thanks for the reviews. I am an Endnote user but I just started work at an institution that has no Endnote license but uses RefWorks… and I was aghast at how horrible the interface is!
    I will certainly try out these other options. I’ve only used Zotero for keeping track of websites so far.

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  13. My university subscribes to Endnote. Since I am about to graduate soon, I decided to try out free reference managers like Zotero, Biblioexpress, WizFolio and Mendeley. I have to say that Zotero is better than Mendeley for me because it is much simpler to retrieve information off the web.

    I can’t give much comments about WizFolio and Biblioexpress as I have yet to really try them. Biblioexpress seems simple to use and WizFolio’s interface looks neat though.

  14. Thanks for the review.

    Maybe it’s just my stupidity, but I have tried Zotero twice, and both times have ended up frustrated. The simple task I cannot accomplish is to browse to a journal article and add it to my library. It doesn’t seem to parse the page and wants me to enter the bibliographic information manually. Like I said, maybe I’m doing something wrong, but it was frustrating that I couldn’t get a simple example to work, so I moved on. Also, I often use a Netbook with a small screen, so the user interface incorporated into Firefox itself is a little difficult to work with. Plus, I also use Chrome as mentioned here.

    I have enjoyed working with CiteULike and have hundreds of papers referenced there.

    Mendeley is intriguing enough that I will give it a try. It seems that since it is a hybrid of Web and Desktop software that it might be the best solution overall. But I’ll have to see how it works in real life. I find it very intriguing that I can annotate PDFs.

  15. Mendelay does look like it will be a great program once it is really up and running. The interface looks a lot more friendly than the zotero interface currently. Of especial interest is the annotation feature and the PDF viewer window.

    One note that may be especially relevant to folks here at savageminds: In all reference management and ‘digital library’ management software now available, there is no ability to tag selected portions of text or to add tags to notes. Ideally, tagging and analyzing one’s paper collection should be similar to coding and analyzing fieldnotes. I’d really like an interface that was more like NVIVO– a hierarchical tag structure, and the ability to pull up text sections across multiple documents using searches and filters. A.nnotate.com is currently the only program that allows something like this, but the interface is still more like a web-tagging program, and is not robust enough for good analytical work.

    Currently, users of Mendeley (or Zotero) only have the option of coding the entire PDF. However, with the event of Google Books (love it or hate it), and as e-readers begin to allow PDF format and annotation/note-taking (and as tablets with touch-screens provide an option for digital reading and note-taking, I now have whole volumes in digital format that require analysis. It is not much use to tag the entire Moby Dick with the label “whale.” Rather, we need to be able to analyze the text itself using tags, and to be able to draw together thematic content from various parts of multiple texts, in order to look for correspondences.

    I hope that the software will catch up to the vision!

    Warmly,
    J

  16. @Steve Piccolo:
    Do you have an example URI that does not work in Zotero? Have you watched the screencasts to know how to use the icon in your address bar to automagically import references from selected sites? If a site isn’t supported, have you tried to import the “EndNote” file the site produces? Zotero’s ability to capture references is second to none.

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